/*
 * aligner.h
 *
 *  Created on: Dec 1, 2012
 *      Author: hxin
 */

#ifndef ALIGNER_H_
#define ALIGNER_H_

#include <string>
#include "refHash.h"
#include <fstream>

using namespace std;

class aligner {
public:
	aligner() {};
	aligner(string hashFileName, string readFileName, string HTFileName = "");
	~aligner();

	void loadHT(int chrNum);
	void alignAll();
	void alignChr(int chrNum);
	void printStat();
private:
	refHash* ht;
	ifstream readFile;
};

#endif /* ALIGNER_H_ */
